Showing : voom • reset
1
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2
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373
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Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
4 months ago richardallenfriedmanbrooklyn ▴ 30
1
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2
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2.5k
views
Non-monotonic voomByGroup plot in Xenium data
XeniumIO voom
4 months ago richardallenfriedmanbrooklyn ▴ 30
4
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8
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1.9k
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Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
4 months ago richardallenfriedmanbrooklyn ▴ 30
1
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2
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3.8k
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Is voomByGroup available in limma?
limmaGUI voom
5 months ago richardallenfriedmanbrooklyn ▴ 30
6
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5
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1.1k
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 11 months ago by 68k • written 11 months ago by • 0
0
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2
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931
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 12 months ago by 53k • written 12 months ago by ▴ 10
1
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8
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2.5k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 13 months ago by • 0
2
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4
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1.2k
views
how limma work with continous variables
GordonSmyth limmaGUI lmFit voom
updated 16 months ago by 53k • written 16 months ago by ▴ 40
4
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4
replies
1.7k
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Using both voom and removeBatchEffect, will they double adjust the data or is it the right way to perform this
limma adjustment voom removeBatchEffect covariates
17 months ago sukeshinik5 ▴ 20
1
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2
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1.1k
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
19 months ago Dylan.Sheerin • 0
0
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2
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806
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 19 months ago by • 0
0
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2
replies
889
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
20 months ago Gimena • 0
5
votes
2
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1.6k
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 2.0 years ago by 53k • written 2.0 years ago by • 0
12
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5
replies
5.1k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 6 months ago by • 0 • written 2.0 years ago by • 0
3
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4
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1.4k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
2.0 years ago pl23 • 0
2
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4
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1.4k
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
2.1 years ago Tyler Sagendorf ▴ 10
5
votes
3
replies
1.3k
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom blocking limma
updated 2.2 years ago by 53k • written 2.2 years ago by ▴ 180
1
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6
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3.7k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 9.1 years ago by ▴ 10
1
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1
reply
2.1k
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
1
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5
replies
2.0k
views
Does voom normalization quantile create difference in DGE genes when distribution of patients is similar (no big differences in quantiles)?
limmaGUI normalization limma voom Normalization
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
0
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1
reply
899
views
How to do PFS after Voom + Limma DGE ?
RNASeqData limma voom PFS DGE
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
0
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1
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1.1k
views
Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
3
votes
4
replies
2.2k
views
Processing data with voom "expression values" and "weights"
limma voom
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
1
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1
reply
1.0k
views
Alternatives to Voom in experiments without replicate
limma edgeR Voom
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
1
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3
replies
1.8k
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR voom normalization DifferentialExpression
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
1
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1
reply
1.4k
views
Voom variance values: Some minor confusion about which variance is fed to lowess when using a design matrix of covariates
voom
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
1
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10
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4.0k
views
multiple voom runs with duplicateCorrelation and negative values in limma
limma voom
3.3 years ago Hilary ▴ 40
2
votes
2
replies
2.0k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
3.4 years ago Yang Shi ▴ 10
2
votes
4
replies
2.1k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 3.4 years ago by 53k • written 3.4 years ago by ▴ 10
5
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6
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2.7k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM avereps voom limma RNASeq
3.4 years ago Yang Shi ▴ 10
2
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4
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2.7k
views
Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
3.4 years ago Yang Shi ▴ 10
2
votes
9
replies
4.1k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
3.5 years ago Peipei • 0
2
votes
2
replies
2.7k
views
Handling NA values in limma's voom design matrix
limma voom design NAs
updated 3.6 years ago by 53k • written 3.6 years ago by ▴ 10
2
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4
replies
5.2k
views
Limma: How to deal with multiple batch effects and what is going on under the hood
limma voom
updated 3.6 years ago by 53k • written 3.6 years ago by ▴ 20
0
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3
replies
2.2k
views
limma voom contrasts
contrasts limma voom
updated 3.8 years ago by 53k • written 3.8 years ago by ▴ 90
0
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3
replies
1.5k
views
Need help with a contrast design for limma with a missing group?
limma VOOM
updated 3.8 years ago by 53k • written 3.8 years ago by ▴ 60
3
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5
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3.7k
views
limma-trend and voom results do not agree
limma limma-trend voom RNASeq
4.1 years ago • updated 4.0 years ago Tyler Sagendorf ▴ 10
3
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2
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2.4k
views
Multi-level design RRBS analysis with voomLmFit
edgeR voomLmFit limma duplicateCorrelation voom
updated 13 months ago by 53k • written 4.0 years ago by • 0
0
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2
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3.3k
views
Mean-variance trend and identifying significant DE with large amount of biological change in expression in time-series data
voom
4.1 years ago • updated 4.0 years ago hmviit • 0
0
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2
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2.0k
views
voom flips the sign relative to log(cpm)
limma limma-voom rnaseq voom
updated 4.2 years ago by 53k • written 4.2 years ago by • 0
0
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1
reply
3.1k
views
limma/voom for protein intensity data
limma proteomics voom
updated 4.2 years ago by ★ 5.0k • written 4.2 years ago by ▴ 70
0
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2
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1.5k
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
4.3 years ago James • 0
0
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2
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1.4k
views
voom-limma workflow for RNAseq samples with very different numbers of counts
voom limma RNASeq
4.7 years ago annadv • 0
0
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2
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8.0k
views
TPM data in limma/voom
voom limma DifferentialExpression edgeR
4.8 years ago RJM • 0
1
vote
1
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2.1k
views
Limma-Voom - Time series experiment with one group (duplicateCorrelation() function)
voom duplicateCorrelation() timeseries limma
updated 5.0 years ago by 53k • written 5.0 years ago by ▴ 10
6
votes
13
replies
7.9k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 3.4 years ago by 53k • written 5.3 years ago by ▴ 60
0
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5
replies
2.0k
views
isoform data, deep sequencing and voom
isoform deep sequencing voom
updated 5.3 years ago by 53k • written 5.3 years ago by ▴ 620
0
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4
replies
1.7k
views
mean-variance trend plots with isoform and gene-level data from tximport
tximport isoform voom
updated 5.4 years ago by 53k • written 5.4 years ago by ▴ 620
1
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4
replies
2.4k
views
How to compare a single RNA-Seq sample with microarray samples?
voom rna-seq microarray
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 10
0
votes
1
reply
1.3k
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 5.5 years ago by 53k • written 5.5 years ago by • 0
166 results • Page 1 of 4
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to James W. MacDonald 68k
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